Stargate: Atlantis Infinity
by KhaosNite911
Summary: Earth and its Off world bases, face complete destruction from the Ori, and SG1 including Jack, travel to Atlantis to save themselves. AU, Major Atlantis crossover. Ch 7 Up! R&R!
1. Earths Destruction

**Title:** Stargate: Atlantis Infinity

**Author:** KhaosNite

**Rating:** T for Teen

**Genre:** Action/Adventure/Humor

**Summary:** Earth and its Off world bases, face complete destruction from the Ori, and SG-1 (including Jack ), travel to Atlantis to save themselves.

**Disclaimer:** I don't own anything of Stargate, just this story plot, and the new commander of the Oddessy for my story, Colonel Dylan Shuttle.

**Spoilers:** SG-1 03-10 "The Pegasus Project" (Though very brief reference in this chpt.)

**A/N:** Crossover with Atlantis, AU, set at the end of S10. In this AU, Jack stays SGC commander and gets promoted after a years worth of base commander service to Major General, but no transfer. Which means No Landry involved. One last thing, any A/N I need to make during the story will be italics and in brackets.

**Chapter 1**

_I can't believe this is it. All our travels and fights have lead us to this very moment. The moment we face utter destruction_, thought Daniel, as from the moment he heard a large fleet of Ori warships entered Earths system. Unfortunately for SG-1, the Ori managed to break through a new connection to their supergate. They had a new plan: instead of convert everyone in the Milky Way to origin, they had decided to destroy Earth and its off-world bases. With the new connection open, the Ori brought a dozen new ships, and scoured the galaxy looking for members of Earth, recognized by their uniforms.

Stargate Command new what was coming when the first report came in from the Oddessy. Unfortunately, they had also discovered one of their teams had been converted into Origin, in an all for nothing attempt to live. With all the information they needed, the Ori planned their new assualt on Earth. With the war failing on all ends, not even the Asgard would survive.

In the final moments of Earths existance, the Oddessy, under command of newly promoted Colonel Dylan Shuttle, beamed SG-1, Jack to the ship. With no time to spare, and seconds to go, the Oddessy entered hyperspace, and set a course for Atlantis.

In the officers mess, every member of SG-1, sat crowed around each other, knowing the Ori had just destroyed Earth. Everything that had been fought for was now lost in the Milky Way. Sam moved closer to Jack, who gave her a hug, to help with the loss. "Thank you sir," Sam managed to say, while crying over the loss of Earth. Jack let go, and kissed her forhead.

"It'll be fine Carter, we just have to move on," Jack said in the sincerest way he could. Teal'C nodded, in agreement with his friend, "General O'Neill is right Colonel Carter, we must move on if we are to deal with the loss of Earth."

Daniel and Cameron, stood together at the window, thinking of what to do now. Daniel turned to face the rest of the team, and tried to smile. Daniel knew, that he had alerted the Ori of Earth, so in essence it was his fault for all of this. But he tried to put it behind him. "Guys, we all have to deal with this loss. Its going to be a hard journey for us all, but we have to make it together," he said, trying to support his friends. Daniel knew very well, from the moment the moment the Ori brought their fleet to Earth, it was over. It was why it was over that bothered him.

_**Flashback**_

Jack, sat frantically in the control room of the SGC, on the red phone talking with the President, about the status of the Ori ships. Pacing back and forth while explaining the situation wasn't going very well. He knew very well the Ori attack would happen very soon. What worried him was how to escape the disaster.

_(Ok for this bit of dialogue, the dots are what the President would be saying over the phone, and since I'm too lazy to write actually dialog, use your imagination, base on whats available. Now on with the show)_

"Sir, I realise whats happening...But we can't attack the Ori ships, they have us far outnumbered and out shipped...I think we should warn Atlantis, and send Oddessy with most of the SGC staff, and SG-1...It seems sir we don't have enough time to warn our off world teams, and we've lost all contact with our off world sites, which means they are dead in the water...very well sir, O'Neill out." Jack finished his conversation with the President, knowing full well what had to be done.

Daniel walked into the control room, holding a sheet of paper, with each of the current off-world teams. Daniel wondered what was going to happen to each team, once they found out Earth couldn't be reached. "Jack, SG-7, and SG-14 are the only teams off world, and they don't return until," Daniel look worried as he looked at the time of their schedule, "Oh god, Five hours from now. Jack, we have to warn them, and quick!"

Jack, stared at Daniel, before walking behind Walter. Jack gave the order to dial the planet SG-7 and 14 were on. The gate spinned around, stopping at each chevron, and locking the seventth. The ever present kawoosh formed, and left behind the event horizon. Jack grabbed the mic.

"SG-7, SG-14, come in, this is General O'Neill requesting **immediate** commincations." he ordered through the mic. For a minute nothing but static, until the voice of Major Peterson came over the radio.

"_General? Your five hours early, whats wrong?_" he asked, with urgency. Jack looked at Daniel, who replied, "Major, get SG-7, and SG-14 home now, Earth and our off-world sites are being attacked by the Ori, I say again, return immediately to Earth!"

Five minutes later, after the communication, SG-7, and SG-14 dialed home, sent their IDC's and enetered the gate room. With no time to have a debriefing, Jack ordered all primary base personell to the gate room, where Jack had to make the speech of his life. It was finally time to leave Earth forever.

_**End Flashback**_

The journey to Atlantis, while only being four days long, gave Jack the time to write his report on the situation about Earth. He knew full well this was harder to live with then when Anubis has destroyed Abydos. Not only had some of his best friends, including General Hammond, been killed by the Ori, he had lost his home, and all true hope of moving on. As he finished writing his report, Colonel Shuttle's voice came over the PA.

"_Attention, this is the Captain. We are approaching Atlantis, and our new home._"


	2. The News

**Title:** Stargate: Atlantis Infinity

**Author:** KhaosNite

**Rating:** T for Teen

**Genre:** Action/Adventure/Humor

**Summary:** Earth and its Off world bases, face complete destruction from the Orin, and SG-1 (including Jack ), travel to Atlantis to save themselves.

**Disclaimer:** I don't own anything of Stargate, just this story plot, and the new commander of the Oddessy for my story, Colonel Dylan Shuttle.

**Spoilers:** SG-1 03-10 "The Pegasus Project" (Though very brief reference in this chpt.)

**A/N:** Crossover with Atlantis, AU, set at the end of S10. In this AU, Jack stays SGC commander and gets promoted after a years worth of base commander service to Major General, but no transfer. Which means No Landry involved. One last thing, any A/N I need to make during the story will be italics and in brackets.

**Chap A/N:** Introduction, and first look at the situation for the rest of the story. Atlantis team introduced, with a shocking revelation about the new lead Atlantis team. Read to find out what that is.

_Previously in Stargate: Atlantis Infinity..._

_**On board the Oddessy**_

"_It'll be fine Carter, we just have to move on," Jack said in the sincerest way he could. Teal'C nodded, in agreement with his friend, "General O'Neill is right Colonel Carter, we must move on if we are to deal with the loss of Earth." _

"_Attention, this is the Captain. We are approaching Atlantis, and our new home._"

And now...

**Chapter 2**

The Oddessy exited hyperspace, and started its approach to Atlantis. On the bridge, Colonel Shuttle was giving orders to the crewman on the bridge, and receiving replies about landing sites, and how long till they landed. SG-1, with Jack, entered the bridge, and stared out the forward window looking onto Atlantis. Daniel gave the same smile he had when SG-1 traveled to Atlantis to start their quest for the Sangrael. _(Note in this universe events have proceeded almost parallel to that in the standard universe, with the exception Jack had made very similar decisions as to what Landry did in the series.)_

Soon after their approach began, the voice of Doctor Weir came over the comm.

"_Oddessy, this is Weir. General, as per your instructions, I haven't spread the news yet, and we are awaiting you all in the city shortly._"

Jack turned to Shuttle, who open the comm lines to Atlantis. Jack smiled, and turned to his former teammates, and replied to Weir. "Doctor, I appreciate what you are doing for us. We will be landing within minutes, and I will prepare to tell everyone the news." Carter, still tearing over the loss, turned to Cam. He gave her a weak smile, knowing full well how the had felt over the loss. Teal'c and Vala, both were tearing up a bit, more so Vala then Teal'c. Surprisingly, Vala turned to Daniel, who was staring at her weirdly for a moment.

"So Daniel, do you think we can explore the city for its marvelous treasures?" Vala asked, in her usual happy voice. The entire team and Shuttle turned to face Vala, all giving her weird looks. Teal'c gave his weird, eyebrow thing.

"What? I mean since we are going to be spending the rest of our lives here, I mean we can certainly search for Atlantis' wondrous treasures," she said, replying to their looks.

Oddessy finally landed on one of the cities landing pads, also noticing the Daedalus was also parked. Jack gave the little hand signal to show his team to get ready to beam down. Everyone from the team, except Daniel and Jack had left the bridge. Daniel had stayed at the front of the bridge staring at Atlantis, wondering whether had he done anything differently in the past two years, this outcome would have been different. He finally had gotten what he wanted, which was a chance to stay in Atlantis, but he didn't want it to be under these circumstances.

Shortly thereafter, SG-1 beamed down to Atlantis' embarkation room, where Doctor Weir, and the Atlantis team, including Lt. Colonel Sheppard, Doctor McKay, Teyla, and Ronin, plus Doctor Beckett were waiting. Doctor Weir, smiled and walked towards SG-1, slowly stretching out her hand for a handshake with Jack. "Welcome back to Atlantis SG-1, I'm glad to see you are all ok," Weir said welcoming the team. Jack accepted the handshake, and nodding at her statement of the team being ok.

"You know SG-1 and I Elizabeth, we usually end our missions without that much of a scratch on us," he said sarcastically, "Now, I think its time we inform everyone of the bad news." Elizabeth nodded, and showed the rest of SG-1 upto the 'control room' of Atlantis.

Weir turned on all-city communications, plus opened comm lines with both the Daedalus and Oddessy and Jack walked upto the console. "Attention everyone, this is Doctor Weir. I'm sure you've heard the news the Oddessy has come to the city, with SG-1. Unfortunetly, they have some terrible news to tell us." Elizabeth announced. Jack nervously started to give the speech about Earth, as the doctor gave him the cue.

"To all members of the Atlantis Expedition, the war in the Milky Way with the Ori, has come to an all-time low. Less then two weeks ago, we received word the Ori had re-opened their connection with the Supergate, and sent a large fleet of their Warships to all our off world sites, and Earth. Now with the tremendous firepower from their super weapons, they destroyed each planet, by firing all at once, and with the strain of 12 Ori ships firing, tore the planets apart. Finally less then a week ago, the Ori fleet entered the Sol system, on a direct course for Earth. Now my team, and most of the SGC staff beamed onto Oddessy before they launched their strike, and managed to get away unharmed. The last we saw of Earth, before we entered Hyperspace was the Ori firing on Earth, and destroying it. It is with my deepest regret to inform you all our home, Earth has been lost. All our families, friends, and loved ones are gone. We are the last survivors of the human race. Before we left, we have managed to bring enough supplies from Earth to supply us for another year or so. After that, we will have to rely on trade with other races to substain us. I wish us the best in our travels, to help us grow and prosper here. General O'Neill, out."

Everyone in the city was very shocked to hear the news of Earth, but decided to block it out and continue their daily business. A few hours after the announcement, Jack met Weir in the briefing room to discuss the creation of Atlantis' new lead team. It took them an hour as to decide its members, and who was leading, but came out smiling. As Jack and Elizabeth exited the briefing room, they went to the mess hall, to find the two teams chatting. "Guys, me and Doctor Weir have an important announcement for all of you. SG-1, and your team Sheppard, are being shut down, as two seperate teams," Jack announced to his friends, and new 'co-workers'. Everyone looked up shocked at what was going on. But Elizabeth lifted her hand, as to finish Jack's announcement. "We have both decided to combine your two teams, and give a new title. From now on you will be known as SG-A, or Stargate-Alpha team." Everyone looked up rather curious as to the decision. What was curious enough was who had been decided to lead the newly formed team. Both John Sheppard, Sam, and Cameron all were the same rank, of Lt. Colonel so one of them leading would be very weird. They knew that neither Daniel, or Mckay were going to lead the team, or any of their alien friends.

"Now this is what is going to be suprising for all of you, as to who is leading you," Jack finished, "I am!" Everyone smiled, and was shocked in amazement, that the ranking officer in Atlantis would be leading them. "And despite me leading the team, I'm also going to be incharge of our military still. Now everyone rest up, Elizabeth has told me she has a surprise for us tomorrow from Dr. Beckett, that I hope will greatly help us here. Until then I will see you later."


	3. Gene Therapy

**Title:** Stargate: Atlantis Infinity

**Author:** KhaosNite

**Rating:** T for Teen

**Genre:** Action/Adventure/Humor

**Summary:** Earth and its Off world bases, face complete destruction from the Orin, and SG-1 (including Jack ), travel to Atlantis to save themselves.

**Disclaimer:** I don't own anything of Stargate, just this story plot, and the new commander of the Oddessy for my story, Colonel Dylan Shuttle, and my Ancient character Jarros.

**A/N:** Crossover with Atlantis, AU, set at the end of S10. In this AU, Jack stays SGC commander and gets promoted after a years worth of base commander service to Major General, but no transfer. Which means No Landry involved.

**Chap A/N:** Daniel gets Ancient Gene Therapy from Dr. Beckett, when something goes wrong.

**Chapter 3**

It seemed with the recent tragedy in the Milky Way, everyone in the city had started to realize, only a day after receiving the news, that everyone, except for those not originally from Earth, had lost their home. Of course it would take some time getting used to, knowing there would be no more check-ins with Stargate Command, or even any communication with loved ones. But this was the price paid for joining the expedition team.

Around lunch time, in Earth standard time, the members of SG-1 made their way to the medical bay, where Doctor Beckett, and a person, human in appearance, awaited them. Unfortunetly for the team, the half of SG-Alpha which featured Colonel Sheppard's team, were out on a mission. Once they returned, they would know what the big news was. As soon as Daniel walked into the med bay, and saw the man beside Doctor Beckett, he had a feeling he knew what was going on.

"Morning people. Now I brought you here today, because in the past few months, I believe with help from my friend here, I have perfected my Ancient gene therapy I started around the time the expedition team arrived. Now Jarros, who was one of the Ancients that survived the Asuran's attack six months ago, has donated a bit of his blood, as I can help extract the necessary coding for someone to receive the gene," Beckett explained, in with his Scottish accent. For Daniel, finally being able to really use the Ancient technology, was almost a dream come true. Jack, who already possessed the gene, had no real use for this, but knew it would be good for Daniel to have.

Vala came forward, with a sort of confused smile on her face, not really sure what Beckett was going on about. "So this Ancient gene thingy, what is it going to do to us? Make us more Ancienty or something?" Beckett turned to Vala, with his answer already thought up. "In a sense love. It allows people who have the Ancient gene, to be able to use Ancient technology, such as the Puddle Jumpers, in our Jumper bay," he replied.

"Question doctor, have you tested it on anyone yet, I mean your new gene therapy?" Daniel asked, a little suspicious. Beckett turned to face Jarros, who in return replied to the question.

"Until now, we haven't had anyone willing to receive the therapy. I have heard, that you Doctor Jackson, are very interested in our technology, and I'm also guessing by that, for you to receive the gene therapy would be an excellent use of your talents with our technology."

"Now if I'm successful in giving the gene therapy, I may be able to give it to you all. The only thing is, that we have a fair amount of people on your team General, who already possess the gene, including yourself," Beckett explained, "Among the Atlantis team, Colonel Sheppard has it, along with Rodney, despite he was my first patient with the gene therapy I started in our beginnings. I believe that we should test it on Doctor Jackson, as he seems most eager to go first."

Jack turned to face Daniel, and found him to be almost ready to jump forward and receive the gene therapy. Doctor Beckett motioned for Daniel to come forward ans sit on the stretcher he had set up. Beckett took the needle, and received some of the serum from his test tube. As he was doing so Daniel rolled up his sleeve, and waited for Carson to approach.

"You should feel a slight tingle in your arm after I inject you. After this I think we should test you right away," Carson noted as he injected the needle into Daniels' arm. He shook a bit, then stood up after Carson removed the needle. Sam smiled at Daniel, hopefully witnessing a turning point in Daniels enthusiasm towards Ancient technology.

"Thank you Carson," Elizabeth said, as she walked into the room with a little smile on your face, "Daniel, if this works, your going to be on of our most vital team members." Daniel nodded at Elizabeth, then turned to face his friends.

"So how about we test my new found 'abilities' on one of the, 'Puddle Jumpers' was it? It could probably give me a bit of flying experience as well," wondered Daniel, eager to test some Ancient technology. Carson nodded, and SG-1 left the medical bay headed towards the Jumper bay. After entering one of the Jumpers, Daniel sat down in the pilot's seat, and activated the Jumper's systems. Slowly and surely, Daniel flew the Jumper out of the top of the bay, over the city. Starting to get used to the ship, Daniel tried a few loops. He almost seemed to be a natural pilot, like Sheppard.

Only a few minutes after attempting the loops, Daniel noticed a problem. "Uh guys, I'm having some problems here. The Jumper isn't responding me anymore," he announced to the rest of the team. With Daniel no longer in control the jumper slowly started to plunge towards the ocean. Daniel collapsed on the floor of the Jumper, shortly after losing his ability to pilot the Jumper. So far any immediate attempts to wake him had failed, and it appeared as though the new gene therapy, unfortunately, had failed.

* * *

A/N: For any Atlantis fans reading this chapter, sorry for really only including Carson and very briefly, Elizabeth 


	4. Ancient Prophecy

**Title:** Stargate: Atlantis Infinity

**Author:** KhaosNite

**Rating:** T for Teen

**Genre:** Action/Adventure

**Summary:** Earth and its Off world bases, face complete destruction from the Ori, and SG-1 (including Jack ), travel to Atlantis to save themselves. Crossover with Atlantis, AU, set at the end of S10. In this AU, Jack stays SGC commander and gets promoted after a years worth of base commander service to Major General, but no transfer. Which means No Landry involved.

**Disclaimer:** I don't own anything of Stargate, just this story plot, and the new commander of the Oddessy for my story, Colonel Dylan Shuttle, and my Ancient character Jarros.

**A/N:** Sorry for the long awaited updated, but Ive been busy, and I havent had a chance to work on this till now.

**Spoilers:** References to The Quest Prt 2. If you havent seen it, on either Sky One (for you Europeans) or if you havent found it on that-video-site-You-love I apologize for ruining your wait.

**Chapter 4**

The Jumper continued to plunge into the water, with Daniel still unconcious. For everyone but Daniel, this feeling of being in a sinking ship was not pleasant. Atleast for the team, the Jumper had not started to leak yet. After checking Daniels pulse, Sam went over to of the compartments, and pulled out a med kit, hopefully finding something to wake him up. As much as she didn't want to admit it, Vala was feeling very scared for Daniels life. Ofcourse it was all part of the job to watch your friends life at risk, much in Merlins lab.

"Sir we need to get Daniel back to the city. He isnt looking to good, and his pulse feels as its getting weaker," Sam reported to Jack and Cam. The team figured immediately after Daniels plunged into what they were assuming was a coma, that Jack was the next person in line to fly the Jumper. After Sam had managed to convince her CO that he needed to fly it, Jack sat down, trying to remember how to fly. Fortunately, the pyshic inter-link with the pilots mind, still existed, and with help from some quick and easy thoughts, Jack managed to get control of the Jumper. He turned to his team, "Piece of cake."

Inside Daniels unconcious mind, the voice of Oma Desala filled his head. Daniel awoke, but not where he had expected himself to be. She appeared on the ramp of the SGC, looking to Daniel rather battered up. His first thoughts was that her battle with Anubis had ended, but why this supposedly eternal struggle ended after only two years time, was just as confusing as trying to wrap your head around the knowledge of the universe. Daniel smiled, not exactly sure what was going on. Upon seeing Oma, wether it really was her or not, he heard his friends trying to save his life. Without the power to say anything to call his friends, he stood their motionless. Everything flashed white and he opened his eyes to see his friends standing over him.

Teal'c bent down and saw Daniel awake from his apparent coma. He watched Daniel slowly get up and Teal'c went to support him. Sam stood back and smiled, along side Vala. Daniel looked around for his glasses and picked them up and turned to see his friends smiling at him. "Anyone wanna tell me what the hell was that?" He asked impatiently. He got up, with some lifting support from Teal'c, and stumbled a bit.

"Thanks Teal'c" Daniel answered, to the assistance given by Teal'c, who in return nodded, "Ok so what happened here? I remember flying the Jumper, then falling over. Like I remember that the whole Jumper started to fail then I..." Daniel closed his eyes and clenched his forehead, and experianced a small headache, "I'm ok..I think. When I was unconcious, I saw Oma."

For most of SG-1, that name had much meaning, but for Cam and Vala, who had not yet experianced who Oma was, and only read about her it didn't mean much.

"Daniel, I swear the report you wrote said that she was in some kind of eternal struggle with Anubis," Jack replied, curious like the rest of the team.

"If her struggle with Anubis has ended, what has become of Anubis?" asked Teal'c, raising his eyebrow. He sat down on one of the benches, beside Cam.

"Well what ever happened I can't be sure. It felt like I saw her for a moment then woke up, but I feel like there was more to this 'vision' of her," Daniel replied, unsure of what actually transpired, "I mean I think she may have told me stuff that the Others WANT us to know, I can't be sure. Its all kind of coming to me, slowly. Let me just think for a moment."

"_Daniel, our struggle has ended, for the will of the struggle between the Ori and the material plane worlds has gone to far. You know as well as I do the Others would never interfere with the matters of the material world, but they have been watching this conflict with great intrest for many of your months. They think it is time to act,"_

"_So basically your saying that you and the Others will actually break your own rule to help us?" asked Daniel, seriously curious of what he had heard._

"_They will not break it, but they have come to realize that in order to preserve themselves they are willing to summon someone resistant to them. The true reason to break the struggle, was to send... Anubis back to the material plane. It was with ALL the will of the Others his memory and his spirit are altered to make him more full of spirit and goodness, so he may join the fight."_

"_Your kidding right? You seriously can't trust him no matter how he has been changed!" exclaimed Daniel._

"-wait, here we go. The Others, want to send someone to help us, and you will never believe who they want to help," explained Daniel, with a worried look on his face. All of SG-1 turned to face Daniel.

"They are sending Anubis back, supposedly with an altered memory and his spirit is full of goodness."

The team looked shocked. Anubis, the last true enemy of SG-1 before the Goa'uld, and the Replicators were destroyed, was supposed to come back and help them? It seemed all to weird, that an old nemesis would help them.

"Wait, wait. Daniel are you serious here?" Sam asked, very curiously.

"Yah, apparently. I mean I don't think the conflict with the Ori is done and over with, despite us being in Atlantis."

"Son of a bitch!" Jack exclaimed, "I swear we got away from those guys. I mean it was bad enough the sangraal turned up to be missing, but now we have to work with Anubis?!"

"I am not as fond of the situation as you are General O'Neill, but perhaps he has changed... hopefully for the better," Teal'c noted, expressing his opinion, despite having the same bad feelings towards Anubis as the rest of SG-1.

"Yah well, I think its time we radioed Atlantis, and get them to beam us out of here," suggested Cam Mitchell, tired of sitting in the still sinking Jumper.

"Agreed," answered Jack, and turned to activate his radio, "Atlantis this is General O'Neill, we are in need of assistance."

"_General, how's Daniel?_" asked Elizabeth, standing in the control room, worried for her friends condition.

"Better, hes awake, and boy does he love a good fairy tale to tell," Jack replied, in a witty sarcastic tone.

"Oh Jack for crying out loud. Elizabeth, what Jack means is that Oma contacted me and they say the conflict with the Ori isn't over, and the Others are sending Anubis, who supposedly will be pure of heart, to help fight the Ori," explained Daniel, coming to his feet, "Now we here would all like someone to beam us out of here, as from what Sam can gather the whole system has fried."

"_Very well Daniel, we will contact the Deadalus and beam your team to the control tower,_" Elizabeth noted to SG-1, and with that she closed the transmission, and contacted the Deadalus. After a few minutes of discussing why it was needed, SG-1 was safely beamed to the control tower of Atlantis.

Oddly enough, shortly after the beam in, the gate started to dial. For whatever reason, the shield was unable to activate, and all teams were placed on high alert, and rushed to the gate. It activated and released its excess energy, and moments later, a figure, dressed in a white cloak, reminiscent of Anubis' came through the stargate, and unhooded himself.

"So this is the Lost City of the Ancients," explained the man, as he saw an approaching SG-1, and Atlantis team, and bowed, "Do not fear, the representative of the Others has arrived.for the service of helping your fight with the Ori."

"Im sorry, and you are?" asked Daniel, approaching carefully, knowing who

"Daniel Jackson, how wonderful to see you again. I am Anubis," Anubis proclaimed, appearing to have shocked the team.


	5. Plan of Attack

**Title:** Stargate: Atlantis Infinity

**Author:** KhaosNite

**Rating:** T for Teen

**Genre:** Action/Adventure

**Summary:** Earth and its Off world bases, face complete destruction from the Ori, and SG-1 (including Jack ), travel to Atlantis to save themselves. Crossover with Atlantis, AU, set at the end of S10. In this AU, Jack stays SGC commander and gets promoted after a years worth of base commander service to Major General, but no transfer. Which means No Landry involved.

**Disclaimer:** I don't own anything of Stargate, just this story plot, and the new commander of the Oddessy for my story, Colonel Dylan Shuttle, and my Ancient character Jarros.

**A/N:** Spoilers for 10.12 "Line in the Sand" 's phase shifiting device. Don't read the latter half of this chap if you don't want to ruin the episode.

**Chapter 5**

The Atlantis team stood at the base of the Stargate, shocked to see that Anubis had entered through the Atlantis gate. Everyone on SG-1 had known Anubis to be the most evil enemy Earth has ever faced, next now to the Ori, but that he was here, now, looking and talking like he was a different person, was shocking. The difference between this Anubis and the one Oma had locked herself in an eternal struggle with, was this Anubis seemed kind hearted, a characteristic not like a Goa'uld.

The security teams guarding the stargate, as Anubis came through, never let their weapons leave their sight.

"Security teams, stand down. Well if it isn't our old pal. Come to try and destroy us again, or is this whole messenger thing honest?" Jack said, really wondering if this was a changed Anubis.

"You are the human, O'Neill. While you may know me from my deeds as being the System Lord, who attacked your world three years ago, I am a new... man. The Others have made me forget most of the acts commited againts the galaxy, but my feelings for them remain, allowing me to realize what has been done, and to remember. My Goa'uld nature has been removed, permanently, but I still call myself by the name of the sysmbiote. However, the Others feel as though I may be the means to stop the Ori. Despite being punished for interfearing, Morgan has watched your progress for trying to get the sangraal, and watched as your quest failed. She believes I can stop them."

"I suppose its honest then. Well how about we go to the briefing room and sit down and discuss all this in more detail, shall we?" proposed Elizabeth, motioning her hand up the stairs. SG-1 and the Atlantis team smiled, briefly and made their way to the briefing room. Upon sitting down, Anubis presented his case and his story about his presence. SG-1, atleast Daniel in particular, found that as he was twice an Ascended being, that even the Others wouldn't show intrest in the affairs of the lower planes. It appear in the fraction of a second that broke the struggle between Oma and Anubis, all the events that changed Anubis gave him the knowledge he needed. He told them that Morgan, after being punished had a chance to prove this fight was worthy, and that was the key factor in their decision.

Anubis had also told them that while Daniel was a Prior, that the Ori had managed to learn the location of Atlantis, and would be at the city in a month. How this was at all possible seemed too complicated for anyone to truly understand, but Daniel assumed that during his 'incursion' an Ascended being was watching over him, hoping it was Morgan Le Fay.

"It seems we really have no choice but to trust you, as its all we can do," noted Daniel, "If your right and the Ori are coming here, we have to get ready for the final fight. We need to make contact with our Milky Way allies, and get some intelligence here."

"Yah, and how do you suppose we do that, hmm?" Rodney asked with a serious face.

"Oh! I know! We go in one of your Puddle jumper things through the gate, and back into the Milky Way, to a planet we know hasn't been converted," suggested Vala, "I mean the Gate Bridge you people built can still be used right?"

"Offcourse it can, but right now we have somewhat more pressing matters then that of the Milky Way. The Wraith are getting a little too pissed with us, and are making another move on Atlantis. Oh and it seems-" Rodney answered, but not before checking the status of the Wraith attack that was again going to strike the city, "What a coincidence, they will arrive at around the same time as the Ori. Isn't that nice."

"So basically, the city is gonna be hit with twice the bad guys?" asked Ronin, a little sceptical of this whole situation.

"Apparently, which means we need to get some more ZPM's to power the city, so we can defend against these attacks," replied Sheppard, "I mean we have the main ZPM in the city, the one we found recently, and I think I heard someone say we brought the one from the Antarctic Outpost."

"What ever you do to defend against this, you appear to have little time to do it," noted Anubis, "They are on the move and preparing for this onslaught."

10 minutes later the briefing ended and everyone exited the room. John showed Anubis to some guest quarters, and then left him for a bit, before returning to his room.

Up in her office, Elizabeth and Jack, were discussing plans for the next month. The first thing they discussed was the city's defenses, that which they realized they had enough power to manage the shield, and power the drone weapons. The problem was, in a month a dozen ships of both Ori and Wraith would be entering orbit, and begin firing upon the city. Now whether or not the shields could withstand that much power wasn't entirely clear at that moment, but the two of them figured Sam, Rodney and Zalenka could figure it out, based on Oddessy sensor readings. The next thing was making contact with the Milky Way to find out what was happening. The other thing that they figured was Jack's team needed to be split back to normal. Having a giant team just didn't quite fit.

"General, with respect, your more of an asset here. I mean you are the ranking military officer here, and despite the fact we lost Earth, your basically incharge," Elizabeth explained, hoping this would click.

Down in the power room, where the ZPM's were located, Sam and Rodney were discussing the power output needed for the shield to run at top efficiency. Laptops open, the discussion turned to what had been power readings Ori and Wraith ships put out in their weapons.

"Look McKay, the power used in the Ori superweapon can easily tear through a Deadalus's shield in 1 maybe 2 hits. Despite it basically took the Koralev out in one blow cause we rushed it, it proves how powerful these things can be. If the shield can protect us from both the Ori and the Wraith, we could be safe," Sam briefed, an interested looking McKay.

"You know, we don't even know if the Wraith and the Ori would join forces to fight us, I mean its possible one could potentially destroy the other," countered Rodney, "but we should also have the Oddessey and the Deadalus to stop them. Shame the Apollo didn't make it off of Earth before the Ori..."

Rodney sighed, thinking that from what he heard of the Apollo, it would have been a formidable match for a wraith hive, and maybe an Ori warship. Since the Ori had invaded the Milky Way, the Asgard had attempted to upgrade their shields. After retrieving sensor readings from both the Oddessy and the Asgard ship that survived, they managed to increase output of shield power to withstand nearly three times more of an Ori main beam. These shields, were modified for the Apollo, and while slightly weaker, would of defended against most of the common enemies of the Milky Way.

"Ok say the Wraith and the Ori do end up fighting each other, whats our worst case scenario?" Sam asked Rodney, thinking about an answer to her own question.

"Worst case, the Ori easily wipe out the Wraith ships, and continue to attack us until they've either learn't their lesson, or.." Rodney replied, only to be cut off from Sam.

"Or they are persistant on retrieving something here," finished Sam, "I mean what has been their primary target when attacking us, uh, SG-1 I mean?"

"I don't know, Dr. Jackson?" answered Rodney, figuring he would be their greatest threat.

"Either that or Vala, I mean we barely managed to break Daniel free from the grasp Adria had on him, and she didn't seem so happy."

"Ok so, if they can't break through the shield they might break off. Say, what about the phase shifting device? I mean since we have all the available power we need, we could cloak the planet," suggested McKay, probably right.

"With a ZPM, it would make the field cover a large distance easily. Do you think we could tie something into the city's sensors that once they've detected the Ori ships, the field is activated?" Sam asked, hoping it was possible.

"Yah, yah, we could. Both the phase shifiting technology and the city is all Ancient, so it could very well work together. Its just how long it would take to write the macro for it."

Over the next couple days, Sam, Rodney, and Radek worked on creating the macro needed for their plan. Carefully, they connected the device to the controls of the sensors, and as soon as that was done, the macro was created. The plan to test it was to launch a sensor drone from the Deadalus, marked with an Ori signature that was created along side the macro.

Up in the control tower, everyone stood awaiting to begin the test.

"Colonel Caldwell, release the drone and have it turn on 10 seconds later, understood?" ordered Jack, speaking over the comm.

"Yes sir," replied Caldwell, "Releasing drone." Out of the port hanger bay, the small beacon drone flew out, and 10 seconds later, near the front of the ship, it activated.

"Drone is on, and a signal is being produced," said a currently satisfied Rodney.

"Sensors have verified the signal, uploading macro," noted Sam, and she entered a few commands on her laptop, and received a confirmation notification on screen.

From the view of the Deadalus and the Oddessey in orbit, the whole planet flashed white, and disappeared. Caldwell turned to his comm officer, giving a go ahead look to open a channel to let Atlantis know their plan succeded.

"Atlantis this is Caldwell, Ill assume you can hear us, and if so, congratulations, we now have our defensive strategy."


	6. Friendly Reunions

**Title:** Stargate: Atlantis Infinity

**Author:** KhaosNite

**Rating:** T for Teen

**Genre:** Action/Adventure

**Summary:** Earth and its Off world bases, face complete destruction from the Ori, and SG-1 (including Jack ), travel to Atlantis to save themselves. Crossover with Atlantis, AU, set at the end of S10. In this AU, Jack stays SGC commander and gets promoted after a years worth of base commander service to Major General, but no transfer. Which means No Landry involved.

**Disclaimer:** I don't own anything of Stargate, just this story plot, and the new commander of the Oddessy for my story, Colonel Dylan Shuttle, and my Ancient character Jarros.

**A/N:** Wonderful things in this chapter. Characters supposed to be dead, aren't, and friendly visits from allies from long ago.

**Chapter 6**

In the Atlantis control tower, every person in the immediate area cheered a bit, knowing they had a viable defense plan, incase the city shield failed. Since the Ori couldn't revert the phase shifting, when the device was being tested in its early stages, the only thing left to do, was to find out what was going on in the Milky Way.

An hour after their test, SG-1, and SGA-1 sat in the briefing room, waiting for Jack and Elizabeth to give them their briefing. They had been 20 minutes late, not normal for those in command. Sam thought it very unlikely for her CO to be late, but it was happening.

As Jack entered, everyone looked surprised to not see Elizabeth with them. It was unlike her to not be present for the briefing, especially when she usually gave them.

"Sorry for being late, but there were some final 'kinks' to be worked out for this mission, that we couldn't work out before now. Today, all of you are going on a fact-finding mission, to find out how far the Ori have come lately. With the attack on Dakara, not long ago, I believe Teal'c, you said the Free Jaffa Nation settled on Chulak, right?" explained a slightly annoyed Jack., from whatever happened between him and Elizabeth not long ago.

"That is correct O'Neill. Those that managed to survive the attack, including Master Bra'tac, fled into the Stargate to Chulak, the original home of the Jaffa Rebellion. I do believe that we may find out the status of the Ori, if we find out how many worlds have been converted, as many of my brothers and sisters are located on many worlds retrieving information on new converted worlds" replied Teal'c.

"Theres also the option of contacting the Tok'ra, knowing them, they have just as many operatives in the field, as the Jaffa might. Last time I spoke with my dad, the Tok'ra joined up with the Free Jaffa on Chulak, to better keep themselves together, despite they still aren't on the friendliest of terms with eachother. Thank god it was them who gave us our intel when the Ori attacked, or we might not of gotten away," suggested Sam, hoping that the Jaffa, the Tok'ra, and more-so her father were allright.

"Either way, we, and yes I do mean I am coming with you," Jack said, before he was about to be interupted by Cam, "-are going off to Chulak to find out what we can, and if it just so happens we may need to, get the Tok'ra Council, and the Jaffa Council out of there. Oh and i almost forgot, Anubis will be joining us, to give some insight into the matter with the Jaffa, and Tok'ra, even though despite his 'change' I'm not sure of him being welcomed. If thats all, your dismissed. Gear up we leave in half and hour."

"Sounds like a plan sir. So Teyla, Ronin, I'm guessing this would be your first time in the Milky Way?" asked Cam, politely.

The two of them smiled, looked at each other and turned to Cam, as they got up from the table. John, move to stand beside them, looking to give his quick insight.

"That would be the case, Colonel Mitchel," replied Teyla, still smiling, "And I'm looking forward to this mission."

"Well from what Ive read about the Jaffa and the Tok'ra, we should get along just fine," noting John, as he and his team left the briefing room, heading towards the armory. Upon arrival, everyone suited up, SG-1 in standard Black BDU's, while the Atlantis team, minus Ronin, wore the 'battle' version of the Expedition uniform, and Ronon in his Satedan uniform. For armaments, everyone grabbed the P90 they preffered, except for Ronon offcourse, grabbing his pistol. Upon suiting up, the teams made their way over to the Jumper Bay, where Jumper Five was picked, and John situated himself in the pilots chair, with Jack beside him in the co-pilots chair. Buckled in, John piloted the Jumper to the base of the Stargate, and inputted the dialing macro.

Within a minute the gate activated, with the Puddle Jumper flying off into the gate. Upon exiting the gate at midway station, a communique was received from Atlantis, from Elizabeth, wishing the team good-luck. Rodney entered the second macro, edited for this mission to send the Jumper to Chulak, and the gate dialed, with Jumper Five entering it once the gate activated. 15 minutes later, Jumper Five exited the Chulak gate, and settled down, in the open space behind the Stargate. Once settled, the team exited the gate, and were welcomed by on-coming Free Jaffa, and three Tok'ra. It wasn't clear until they got close, but Sam knew immedietly who two of the Tok'ra were. Teal'c on the other hand, recognized the two Jaffa.

"Dad! Martouf! Oh my god its been for ever," exclaimed Sam, rushing to hug her father. Martouf, stood beside Jacob, and smiled.

"Tek'ma'tae Bra'tac, Rak'nor. It is good to see that you are well," greeted Teal'c, to his former Jaffa Master and friends.

"Jacob, Bra'tac, Martouf, allow me to introduce Colonel Sheppard, Dr. Mckay from Earth, currently on our Atlantis Expedition, and Teyla Emmagen, and Ronon Dex, natives to the Pegasus Galaxy," Jack introduced the Atlantis team members.

"It is an honour to meet such people, from the Pegasus Galaxy," greeted a smiling Bra'tac, shaking hands with Teyla and Ronon.

"So these are the Jaffa and Tok'ra you were telling us about," Ronon noted towards Jack.

Sam broke her hug from her dad and moved to Martouf, who gave him a quick kiss on the cheek. She broke off, still smiling, when Jacob realized the visit wasn't one of a friendly nature.

"I take it you are here on a visit just to say 'Hi' are you?" asked Jacob, who stopped smiling. The moment then turned to a serious matter.

"No, and we learned some pretty important stuff from someone who's gonna be crucial to the destruction to the Ori. Now some of you aren't gonna like this but Anubis is gonna be the deciding factor for this war," replied, and proclaimed Daniel, worrying for the response of Bra'tac and the Tok'ra, "Now from what he told us, the Others, the collective group of Ascended Ancients, sent him back to our plain to help us fight the Ori. The other thing they did was make him good in spirit, and he can't really remember his past, but he decided to keep his Goa'uld name. I realize this isn't the best place to walk, so what, should we go inside?"

"That would be best Daniel," replied Jacob, "Come. We have some important news for you to."

Jacob motioned towards the city, and the team follow suit, Sam walking with her dad, and Teal'c following beside Bra'tac. They reached the city, which looked renewed, and approached the castle, which all of SG-1 recognized was the prison they were in, in the beginning of their adventures.

Upon entering, they were instructed to go to the large council room, which looked oddly familiar to everyone. SG-1 was right of course, it was the same prison room SG-1 had been in, when they were captured by Apophis so long ago. But now it had been converted into a large council room, and obviously redecorated from the the old layout.

"Now that we have a place to talk, I say lets get to it. Recently the Ori have nearly stopped converting planets, as far as our operatives can tell. And mind you, this is in the past couple weeks. Now we managed to gather the intelligence they were to attack Earth and your offworld sites. Thats when we lost contact with the Ori, and we haven't heard of them converting planet's since," informed Jacob Carter, who lowered his head, releasing Selmak's control, "Our operatives cannot figure out why they have abandoned their quest to convert us."

"They've found out the location of Atlantis, are are on their way to attack us there, and will be there in a month," responded Jack, "Now as far as we can tell we can defend the city, but we also discovered a large Wraith armada also on their way, also in the timeframe of about a month."

The Tok'ra and Jaffa council members looked upon the faces of SG-1 and the Atlantis team, in shock, but also in a state of relief for the Milky Way.

"Unfortunetly, neither the Free Jaffa or the Tok'ra can assist you in that matter. However, our operatives, managed to find someone of importance to your team. A Tok'ra operative, Torin, who was secretively watching Langara, managed to find one person, who had not converted to Origin, and fortunetly not killed. I think you'll recognize him," replied Bra'tac, as around the corner, Jonas Quinn, walked down the steps looking rather battered, even after being on Chulak for a few months. This was quite a surprise for SG-1, believing that everyone on Langara had been converted to Origin. During the final bit of the conference, it was revealed Jonas was conducting a research mission in the greater area of the planet, and as he returned, he knew something wasn't right...

"And thats when I barely managed to escape through the Stargate," finished Jonas, "By the time I got to the complex with our Stargate, our High Minister was there, with a Prior, telling of their religion. When he refused to heed the Prior's demand for us to follow him in Origin, he killed our Miniser. The rest of our people soon followed with him. They evacuated the Stargate, and the Tok'ra, Torin, found me and brought me here. When the Ori soldiers heard the Stargate activate, they managed to kill Torin, and they didn't see the gate address, so we've been lucky."

"Jonas, as much I'm sure you've gotten used to staying here with the Tok'ra, I want you to come with us, back to Atlantis," Jack proposed to Jonas, hopefully receving a yes.

"You mean the City of the Ancients, Atlantis?" asked a surprised Jonas, never expecting to ever go to Atlantis, and wondering what it might be like.

"That's the one," responded Jack.

"So when are we leaving?" piped up Jonas, quite excited by the looks of things.

"As soon as your ready," replied Sam.

"Great lets go!" exclaimed Jonas, sitting up, smiling widely.


	7. Important Research

**Title:** Stargate: Atlantis Infinity

**Author:** KhaosNite

**Rating:** T for Teen

**Genre:** Action/Adventure

**Summary:** Earth and its Off world bases, face complete destruction from the Ori, and SG-1 (including Jack ), travel to Atlantis to save themselves. Crossover with Atlantis, AU, set at the end of S10. In this AU, Jack stays SGC commander and gets promoted after a years worth of base commander service to Major General, but no transfer. Which means No Landry involved.

**Disclaimer:** I don't own anything of Stargate, just this story plot, and the new commander of the Oddessy for my story, Colonel Dylan Shuttle.

**A/N:** Wonderful things in this chapter. Characters supposed to be dead, aren't, and friendly visits from allies from long ago.

**Chapter 7**

Jonas situated himself in a seat of the Puddle Jumper, a bright smile over his face, much like when he was with SG-1 for the first time. For Jonas, he felt like the young man he was, so curious about the galaxy. When he looked at Teal'c he nearly thought he was someone else, because of all the hair he had. Sheppard sat in the pilots chair, and started up the Jumper. Turning back he smiled at Jonas.

"So your the guy who was on SG-1 during Daniel's Ascension?" John asked Jonas, who was admiring the Puddle Jumper. Still smiling he turned to face John.

"Yah, thats me alright. God look at this thing! I mean, I can't believe I'm actually in an Ancient craft" responded Jonas, still admiring the ship.

"I'm Lt. Colonel Sheppard, and thats Teyla Emmagen, Ronon Dex, and Rodney McKay," introducing Johns team to Jonas.

Rodney smiled at Jonas, "Oh, we've met already. The alien with the crazy naquadah, who helped saved Earth from Anubis a few years ago."

"You still remember that then?" questioned Jonas.

"Offcourse I'd remember you. I mean first Carter outsmarts me, then an alien? That doesn't go to well on my record," replied a slightly annoyed Rodney.

"Ok, now that we have intros out of the way, Rodney would you be so kind as to start dialing the gate?" noted John, to Rodney, who graciously grabbed his laptop.

"Ah yes, sorry about that," replied Rodney, typing on his laptop the command to start the macro, "Macro's active, and we can dial the gate."

At the foot of the Jumper, stood Martouf, Jacob and Bra'tac. Sam walked to the base of the Jumper, and gave her father a hug, and a kiss on the cheek. Her dad returned the favour, and they broke off, and Sam stood smiling at Martouf.

"It was good to see you Samantha. I hope in the future I may be able to visit you at Atlantis," hoped Martouf, who returned the smile.

For good-byes, at least this time SG-1 was saying good-bye to the Tok'ra at their home, instead of The Tok'ra saying good-bye on Earth. John powered the Jumper up, and started dialing. After the woosh, the Jumper entered the gate, and left the Milky Way, back to their 'new' home. Back in Atlantis, Elizabeth, and Carson were examining Anubis, who appeared to be working on something in one of the labs in Atlantis. From the looks of what he was doing, he was building something, that probably SG-1, might of recognized.

Over her radio, Elizabeth received a comm, from the control tower. General O'Neill and his team had returned. She made her way back to the control tower, and upto the Jumper bay to meet them, when she say an unfamiliar face amongst them. She approched the man, who was looking very happy, admiring the city of Atlantis.

"Greetings, I'm Doctor Elizabeth Weir, leader of the Expedition. And you are?" introduced Elizabeth.

Still looking around, Jonas finally managed to break his awe to answer Elizabeth.

"Oh, I'm Jonas Quinn. I was a member of SG-1 when Dr. Jackson Ascended," replied Jonas.

"Doctor, instead of having a full normal debriefing, I'll have a report written up, so we can get Jonas situated with some quarters," insisted Jack.

Jack and the rest of the team returned to the armoury, and deposited their gear, and headed off to do stuff on their own.

**Four days later...**

Daniel sat in his new office, reading a collection of books he had managed to take with him, before Earth s disaster, and found himself thinking about a realization he had from reading this. Jonas walked in on him, and saw he was flipping through some other books.

"Jonas! I think I found something pretty intresting here," Daniel motioned for Jonas to come over to him, "Now, when you on Earth, did you ever read anything about Earth mythology, concerning Zeus?"

Jonas pondered for a moment, before replying, "Yah, I think so. He was the supreme ruler of Mount Olympus, and lord of the gods there, and also that he threw bolts of lightning."

"Ok, about a year before we found you, on a planet called Velona, they created a weapon with help from an Ancient, known as Orlin. Now as we tried to use the weapon, the Others stepped in as a collective, and destroyed the machine with a bolt of lightning. Now as you said, in most works that feature Zeus, he had the ability to throw bolts of lightning at those who had wronged him, or the Greeks. With that in mind, I think Zeus might have been a Ancient, or maybe an Ascended Being, who took human form and retained the power of an Ascended, " explained Daniel.

Confused, Jonas finally thought of a response, "Ok, that doesn't make sense. In your mythology, Cronus was the _father_ of Zeus. How could a Goa'uld of been a father of an Ancient?"

Daniel pondered, before running off in order to find Jack. He found him sitting in his office, writing up a briefing for SG-3's next mission. He turned to see Daniel catching his breath.

"Daniel..."

"Jack, I think I found something important. We need to go back to the ruins at P2C-391, as soon as possible," Daniel demanded, still catching his breath.

"Thats the planet with the Zeus statue right?" Jack asked, trying to remember, and Daniel nodded, "Daniel, you know you we still have to worry about the Ori. They know we escaped, and they know exactly how to find us. What do you think we can find on Three-Nine-One thats so important?," responded Jack, mildly skeptical.

"An Ancient who can stop us fight the Ori," Daniel reply, finnally finishing to catch his breath.


End file.
